Bacteriophages as Environmental Reservoirs of Antibiotic Resistance

Calero-Cáceres, William; Ye, Mao; Balcázar, José Luís

doi:10.1016/j.tim.2019.02.008

Cited by 125 publications

(93 citation statements)

References 66 publications

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“…With respect to antibiotic resistance genes (ARGs), their presence within phage genomes is debated. Most reports are flawed by either excessive bacterial DNA contamination of the virome samples [71][72][73][74] or inappropriate thresholds used for the similarity search against ARG databases. 75 When both pitfalls were eliminated, ARG were rare in phage genomes (around or <1 gene among 10 5 genes analyzed, on phage genomes and phage metagenomic contigs respectively), 76 confirming an ancient observation.…”

Section: Prophage Inductionmentioning

confidence: 99%

New insights into intestinal phages

et al. 2020

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The intestinal microbiota plays important roles in human health. This last decade, the viral fraction of the intestinal microbiota, composed essentially of phages that infect bacteria, received increasing attention. Numerous novel phage families have been discovered in parallel with the development of viral metagenomics. However, since the discovery of intestinal phages by d'Hérelle in 1917, our understanding of the impact of phages on gut microbiota structure remains scarce. Changes in viral community composition have been observed in several diseases. However, whether these changes reflect a direct involvement of phages in diseases etiology or simply result from modifications in bacterial composition is currently unknown. Here we present an overview of the current knowledge in intestinal phages, their identity, lifestyles, and their possible effects on the gut microbiota. We also gather the main data on phage interactions with the immune system, with a particular emphasis on recent findings.

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Section: Prophage Inductionmentioning

confidence: 99%

New insights into intestinal phages

et al. 2020

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“…Marie-Agnès Petit (MICALIS, Jouy-en-Josas, France) and her team previously showed that antibiotic resistance genes (ARG) were infrequent in phage genome and virome contigs [21]. Conversely, recent studies suggested that pig fecal samples could be rich in viral ARG, although these conclusions could be impaired due to bacterial DNA contamination [22,23]. Fourteen pig (five piglets and nine adults) fecal samples were processed to obtain clean and pure pig viromes.…”

Section: Introductionmentioning

confidence: 99%

“French Phage Network” Annual Conference—Fifth Meeting Report

Laumay

Chaïb

Linares

et al. 2020

Viruses

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Attracting about 100 participants, the fifth edition of our French Phages.fr annual conference was once more a success. This year’s conference took place at the Institute for Structural Biology on the European Electron and Photon Campus in Grenoble, 8–9 October 2019. Similar to previous years, our meeting gathered scientists mainly working in France, from academic labs and hospitals as well as from industry. We also had the pleasure of welcoming attendees from different European countries and even beyond. The conference was divided into four sessions: Ecology and Evolution, Phage Therapy and Biotechnology, Structure and Assembly and Phage–Host Interaction, each opened by a keynote lecture. The talks, selected from abstracts, gave the opportunity for young scientists (especially students and post-docs) to present their project and results in a friendly atmosphere. Poster sessions also favoured interactions and discussions between young researchers and more senior scientists. Here, we provide a summary of the topics developed during the conference.

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“…In a recent study, none of the ARGs retrieved from viral contigs expressed antibiotic resistance when cloned into E. coli [21], leading to the conclusion that numbers of phagecarried ARGs are overestimated. Nevertheless, as ARGs continue to be detected in phage isolates and viromes from diverse environments [20,[23][24][25][26], whether phages are important reservoirs of ARGs or not is still on debate.…”

Section: Introductionmentioning

confidence: 99%

Freshwater Viral Metagenome Reveals Novel and Functional Phage-borne Antibiotic Resistance Genes

Moon

Kang

Park

et al. 2019

Preprint

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BackgroundAntibiotic resistance developed by bacteria is a significant threat to global health. Antibiotic resistance genes (ARGs) spread across different bacterial populations through multiple dissemination routes, including horizontal gene transfer mediated by bacteriophages. ARGs carried by bacteriophages are considered especially threatening due to their prolonged persistence in the environment, fast replication rates, and ability to infect phylogenetically remote bacterial hosts. Several studies employing qPCR and viral metagenomics have shown that viral fraction and viral sequence reads in clinical and environmental samples carry many ARGs. However, only a few ARGs have been found in viral contigs assembled from metagenome reads, with most of these genes lacking effective antibiotic resistance phenotypes. Owing to the wide application of viral metagenomics, nevertheless, different classes of ARGs are being continuously found in viral metagenomes acquired from diverse environments. As such, the presence and functionality of ARGs encoded by bacteriophages remain up for debate.ResultsWe evaluated ARGs excavated from viral contigs recovered from urban surface water viral metagenome data. In virome reads and contigs, diverse ARGs, including polymyxin resistance genes, multidrug efflux proteins, and β-lactamases, were identified. In particular, the novel β-lactamases blaHRV-1 and blaHRVM-1 found in this study had unique sequences, forming distinct clades of Class A and subclass B3 β-lactamases, respectively. Minimum inhibitory concentration analyses for E. coli strains harboring blaHRV-1 and blaHRVM-1 and catalytic kinetics of purified HRV-1 and HRVM-1 showed reduced susceptibility to penicillin, narrow- and extended-spectrum cephalosporins, and carbapenems. These genes were also found in bacterial metagenomes, indicating that they were harbored by actively infecting phages.ConclusionOur results showed that viruses in the environment carry as-yet-unreported functional ARGs, albeit in small quantities. We thereby suggest that environmental bacteriophages could be reservoirs of widely variable, unknown ARGs that could be disseminated via virus-host interactions.

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Bacteriophages as Environmental Reservoirs of Antibiotic Resistance

Cited by 125 publications

References 66 publications

New insights into intestinal phages

New insights into intestinal phages

“French Phage Network” Annual Conference—Fifth Meeting Report

Freshwater Viral Metagenome Reveals Novel and Functional Phage-borne Antibiotic Resistance Genes

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